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Yorodumi- PDB-2wop: Clavulanic acid biosynthesis oligopeptide binding protein 2 compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wop | ||||||
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Title | Clavulanic acid biosynthesis oligopeptide binding protein 2 complexed with arginine | ||||||
Components | CLAVULANIC ACID BIOSYNTHESIS OLIGOPEPTIDE BINDING PROTEIN 2 | ||||||
Keywords | PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-PEPTIDE COMPLEX / SOLUTE-BINDING PROTEIN / CLAVULANIC ACID BIOSYNTHESIS / OLIGOPEPTIDE BINDING PROTEIN | ||||||
Function / homology | Function and homology information clavulanic acid biosynthetic process / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | STREPTOMYCES CLAVULIGERUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | MacKenzie, A.K. / Valegard, K. / Iqbal, A. / Caines, M.E.C. / Kershaw, N.J. / Jensen, S.E. / Schofield, C.J. / Andersson, I. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Crystal Structures of an Oligopeptide-Binding Protein from the Biosynthetic Pathway of the Beta-Lactamase Inhibitor Clavulanic Acid. Authors: Mackenzie, A.K. / Valegard, K. / Iqbal, A. / Caines, M.E.C. / Kershaw, N.J. / Jensen, S.E. / Schofield, C.J. / Andersson, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wop.cif.gz | 130.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wop.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 2wop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wop_validation.pdf.gz | 454.6 KB | Display | wwPDB validaton report |
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Full document | 2wop_full_validation.pdf.gz | 456.9 KB | Display | |
Data in XML | 2wop_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 2wop_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/2wop ftp://data.pdbj.org/pub/pdb/validation_reports/wo/2wop | HTTPS FTP |
-Related structure data
Related structure data | 2wokC 2wolSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 62065.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8KRB4 |
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#2: Chemical | ChemComp-ARG / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | pH: 8 / Details: PH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→62.5 Å / Num. obs: 61692 / % possible obs: 92.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 4.8 / % possible all: 60 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WOL Resolution: 1.7→62.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.581 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→62.5 Å
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Refine LS restraints |
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